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How many fans do you have and where are tehy connected?
One big fan from on the back, one fan on the back of hot-swap hdd enclosure, and cpu fan.
Make sure the back fan is plugged into SysFan 6, front fan into SysFan 1, and processor fan is in CPU 1. See http://www.intel.com/support/motherboards/server/s5000vsa/sb/CS-022691.htm , Quick Start Guide - Back, under "Making Connections to the Server Board"
Then re-run the FRU update, if the issue persists.
Thanks, back fan was connected to sysfan5, now connected to susfan6 and works ok.